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Nitrogen Metabolism Genes from Temperate Marine Sediments

Reyes, Carolina, Schneider, Dominik, Lipka, Marko, Thürmer, Andrea, Böttcher, Michael E., Friedrich, Michael W.
Marine biotechnology 2017 v.19 no.2 pp. 175-190
Archaea, Beggiatoa, Nitrobacter, Nitrosococcus, Nitrosomonas, Thiothrix, ammonia, ammonification, ammonium, bacteria, denitrification, genes, marine sediments, metagenomics, models, nitrates, nitrification, nitrites, nitrogen, nitrogen metabolism, oxidation, proteinases, ribosomal RNA, Baltic Sea, North Sea
In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO₃ ⁻ was present in the top 5 cm below the sediment-water interface at both sites. NH₄ ⁺ increased with depth below 5 cm where it overlapped with the NO₃ ⁻ zone. Steady-state modelling of NO₃ ⁻ and NH₄ ⁺ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO₃ ⁻ reduction to NH₄ ⁺ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO₃ ⁻ reduction to NO₂ ⁻ or NH₄ ⁺ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.